Deciphering the three-dimensional atomic structure of solid-solid interfaces in core-shell nanomaterials is the key to understand their remarkable catalytical, optical and electronic properties. Here, we probe the three-dimensional atomic structures of palladium-platinum core-shell nanoparticles at the single-atom level using atomic resolution electron tomography. We successfully quantify the rich structural variety of core-shell nanoparticles including bond length, coordination number, local bond orientation order, grain boundary, and five-fold symmetry, all in 3D at atomic resolution. Instead of forming an atomically-sharp boundary, the core-shell interface is atomically diffuse with an average thickness of 4.2 Å, irrespective of the particle’s size, morphology, or crystallographic texture. The high concentration of Pd in the interface is highly related to the electric double layers of the Pd seeds. These results advance our understanding of core-shell structures at the fundamental level, providing potential strategies into nanomaterial manipulation and chemical property regulation.